scholarly journals Subunits I and II of Dictyostelium cytochrome c oxidase are specified by a single open reading frame transcribed into a large polycistronic RNA1The sequence data reported in this paper have been submitted to the EMBL/GenBank/DDBJ data base under the accession number X81884.1

1997 ◽  
Vol 1320 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Rossella Pellizzari ◽  
Christophe Anjard ◽  
Roberto Bisson
Keyword(s):  
Cytochrome C ◽  
Data Base ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Open Reading Frame ◽  
Single Open Reading Frame ◽  
Accession Number ◽  
Reading Frame

scholarly journals coil: an R package for cytochrome c oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation

Genome ◽  
2020 ◽  
Vol 63 (6) ◽  
pp. 291-305 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Sarah J. Adamowicz
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Dna Barcode ◽  
R Package ◽  
Data Generation ◽  
Error Identification ◽  
Reading Frame ◽  
Biological Contaminants ◽  
And Function

Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5′ region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil ), an R package for the pre-processing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.

scholarly journals coil: an R package for cytochrome C oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation

2019 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Sarah J. Adamowicz
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Dna Barcode ◽  
R Package ◽  
Data Generation ◽  
Error Identification ◽  
Reading Frame ◽  
Biological Contaminants ◽  
And Function

AbstractBiological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The five-prime region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil (https://CRAN.R-project.org/package=coil), an R package for the pre-processing and error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10,000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.

Molecular and Ultrastructural Analysis of a Porocephalus sp. (Arthropoda: Pentastomida) Removed from a Rattlesnake

2021 ◽  
Vol Vol 66 (1) (January (1)) ◽  
pp. 1-5
Author(s):  
Jerome Goddard ◽  
Gerald Baker ◽  
Petra Jericke ◽  
Lawrence Birchman ◽  
Ethan Woodward ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Adult Female ◽  
Sequence Data ◽  
Molecular Data ◽  
Ultrastructural Analysis ◽  
Oxidase Subunit ◽  
Data Support ◽  
Partial 18S

Ultrastructural and molecular data are provided from a single adult female pentastomid opportunistically collected from a road-killed rattlesnake in Russell, KS. Ultrastructural data consisted of light and SEM microscopy of the pentastomid and its eggs, while molecular data consisted of partial 18S and 28S ribosomal sequences and a partial cytochrome c oxidase subunit 1 sequence from the same specimen used for SEM. Ultrastructural and molecular data support generic identification of the pentastomid as Porocephalus sp. These molecular data were also used with previously published pentastomid sequence data for a concatenated phylogenetic analysis, which support the current, morphology-based taxonomic placement of the genus.

scholarly journals Expression of antibodies using single open reading frame (sORF) vector design

mAbs ◽  
2013 ◽  
Vol 5 (4) ◽  
pp. 595-607 ◽  
Author(s):  
Wendy R. Gion ◽  
Rachel A. Davis-Taber ◽  
Dean A. Regier ◽  
Emma Fung ◽  
Limary Medina ◽  
...  
Keyword(s):  
Open Reading Frame ◽  
Single Open Reading Frame ◽  
Reading Frame

DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae)

2006 ◽  
Vol 36 (2) ◽  
pp. 337-350 ◽  
Author(s):  
Shelley L Ball ◽  
Karen F Armstrong
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Insect Pest ◽  
Reference Sequence ◽  
Identification System ◽  
Pest Species ◽  
Dna Barcodes ◽  
Data Set

Reliable and rapid identification of exotic pest species is critical to biosecurity. However, identification of morphologically indistinct specimens, such as immature life stages, that are frequently intercepted at borders is often impossible. Several DNA-based methods have been used for species identification; however, a more universal and anticipatory identification system is needed. Consequently, we tested the ability of DNA "barcodes" to identify species of tussock moths (Lymantriidae), a family containing several important pest species. We sequenced a 617 base pair fragment of the mitochondrial gene cytochrome c oxidase 1 for 20 lymantriid species. We used these, together with other Noctuoidea species sequences from GenBank and the Barcoding of Life Database to create a "profile" or reference sequence data set. We then tested the ability of this profile to provide correct species identifications for 93 additional lymantriid specimens from a data set of mock unknowns. Of the unknowns, 100% were correctly identified by the cytochrome c oxidase 1 profile. Mean interspecific sequence (Kimura 2-parameter) divergence was an order of magnitude greater (14%) than mean intraspecific divergence (<1%). Four species showed deeper genetic divergences among populations. We conclude that DNA barcodes provide a highly accurate means of identifying lymantriid species and show considerable promise as a universal approach to DNA-based identification of pest insects.

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